Документ взят из кэша поисковой машины. Адрес оригинального документа : http://mouse.belozersky.msu.ru/npidb/data/pdb_new/hmm/4c2u.pdb1.pdb.hmm.txt Дата изменения: Fri Nov 22 18:29:05 2013 Дата индексирования: Fri Feb 28 22:19:44 2014 Кодировка:

# pfam_scan.pl, run at Fri Nov 22 18:29:02 2013
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see .
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /data/npidb/pdb/pdb_new/fasta/4c2u.pdb1.pdb.fas
# searching against: /mnt/databanks/pfamdata/Pfam-A.hmm, with cut off -E 0.001 --domE 0.001
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
#

4c2u_A 10 127 10 136 PF00580.16 UvrD-helicase Domain 1 140 315 110.1 1.2e-31 1 CL0023
#HMM lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelle
#MATCH lnp q +a+ +++gp lv+A+AGsGKT++l++ri++li + +++p +il+vTFTnkAa+E++eR +++ a ++++sT+Hs + +il+++ ++igl+++f i+d++d q+ ++ke++
#PP 699*******************************************************************97.................59**********************************.....6777777665
#SEQ LNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGA-----------------GDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDD-----QLDIIKEVMG
#CS SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHC
4c2u_A 136 273 130 273 PF00580.16 UvrD-helicase Domain 180 315 315 129.6 1.4e-37 1 CL0023
#HMM eelrelvskakekqlspkelkkaf..ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflkkkkdfk
#MATCH +r ++++ak+++ +p +l++ ++ ++++ae++++y+ +kk +na+Df dl+ ++++l++e + ++++++++ k+i++DEyQDTn++Qy++ +llas+ ++l++vGDp+QsIY+FRgAdi+++l ++kd++
#PP 56788899999999999988886666788899999****************************************************************************************************995
#SEQ RVIRGIIDRAKSNLWTPDDLDRSRepFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYP
#CS CHHHHHHHHHHHTTCCTTHHTCXX..TSSSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHHHHHHST
4c2u_A 278 622 278 623 PF13361.1 UvrD_C Domain 1 350 351 293.0 3.7e-87 1 CL0023
#HMM iiLeeNYRStkeileaankllenafpednkdrykkgllseskdgeekislleaenereeaefianeikkleeknisakdiavLvRsnrqarnleeaLksagiPyklvgqfkfferkeikdllallklianpsdsislkrilkspprgigdktleaiesyakekdlllleilkndevktseelsakaskklkaflelieklqnklkeasglselvekiveetglkelltkd.eegeeklenlrellellkeldnknknsresLldfleelslsseeeeee...vilrtkkdaVkimTvHkaKGLEfpvVFlsgleegtfPsersi.ekeenleeErRlfYVAiTRAkkqLyltaak
#MATCH xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF++Le NYRS++++leaankl+ e+n++r +k+l +++ g +++++ a ++r+e ++a+ +++l+ ++ ++++a+L+R+n+q+r +ee L++ +iP ++vg++ f++r ei+d+la+ +l +np d+++l+ri+ +p rgigd+ l+++ + a +++ ++l+++ ++++ ++ + k+ +f l+e + + +++ +++++++ ++e +g+ +ll+++ +eg+ +lenl+el+++++e++++++n s+ dfl + +l s ++ ++ + +daV++mT+H+aKGLEfpvVF++g+e+g +Ps+ i e +eeErRlfYV+iTRA+++L +taa+
#PP 589******************.....******************.******************************************************************************************************************************7...56666666777777799999999998.557789***********************************************************99987766655534356667779**********************************99**************************987
#SEQ YMLEHNYRSSARVLEAANKLI-----ENNTERLDKTLKPVKEAG-QPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACA---NAAEQNILDRGAHKATEFAGLMEAMS-EAADNYEPAAFLRFVMETSGYLDLLRQEgQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRtkaENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIaEGPSGIEEERRLFYVGITRAMERLLMTAAQ
#CS EEE-EESSS-HHHHHHHHHHHCC---TTSSSSCCCEEEESSTEEESSEEEEEECSHHHHHHHHHHHHHHHHHTTS-GGGEEEEESSCHHHHHHHHHHHHTTS-EEESSSSCGGGSHHHHHHHHHHHHHH-TTSHHHHHHHTTSTTCTTTHHHHHHHHHHHHHTTS-HHHHHH..HCHHTSCSTCHHHHHHHHHHHHHHHHHHHHCTTS-HHHHHHHHHHHTTHHHHHHCS.HHHHHHHHHHHHHHHHHHHHCCCSCSSCHHHHHHHHHHHHTCCCTSTT...SXXTTCCGSEEEEECGGGTT--EEEEEEETTBTBTTTBHHHH.HHHHHHHHHHHHHHHHHHTEEEEEEEEEEC
4c2u_D 10 127 10 136 PF00580.16 UvrD-helicase Domain 1 140 315 110.1 1.2e-31 1 CL0023
#HMM lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelle
#MATCH lnp q +a+ +++gp lv+A+AGsGKT++l++ri++li + +++p +il+vTFTnkAa+E++eR +++ a ++++sT+Hs + +il+++ ++igl+++f i+d++d q+ ++ke++
#PP 699*******************************************************************97.................59**********************************.....6777777665
#SEQ LNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGA-----------------GDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDD-----QLDIIKEVMG
#CS SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHCCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHC
4c2u_D 136 273 130 273 PF00580.16 UvrD-helicase Domain 180 315 315 129.6 1.4e-37 1 CL0023
#HMM eelrelvskakekqlspkelkkaf..ekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflkkkkdfk
#MATCH +r ++++ak+++ +p +l++ ++ ++++ae++++y+ +kk +na+Df dl+ ++++l++e + ++++++++ k+i++DEyQDTn++Qy++ +llas+ ++l++vGDp+QsIY+FRgAdi+++l ++kd++
#PP 56788899999999999988886666788899999****************************************************************************************************995
#SEQ RVIRGIIDRAKSNLWTPDDLDRSRepFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYP
#CS CHHHHHHHHHHHTTCCTTHHTCXX..TSSSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHHHHHHST
4c2u_D 278 622 278 623 PF13361.1 UvrD_C Domain 1 350 351 293.0 3.7e-87 1 CL0023
#HMM iiLeeNYRStkeileaankllenafpednkdrykkgllseskdgeekislleaenereeaefianeikkleeknisakdiavLvRsnrqarnleeaLksagiPyklvgqfkfferkeikdllallklianpsdsislkrilkspprgigdktleaiesyakekdlllleilkndevktseelsakaskklkaflelieklqnklkeasglselvekiveetglkelltkd.eegeeklenlrellellkeldnknknsresLldfleelslsseeeeee...vilrtkkdaVkimTvHkaKGLEfpvVFlsgleegtfPsersi.ekeenleeErRlfYVAiTRAkkqLyltaak
#MATCH xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF++Le NYRS++++leaankl+ e+n++r +k+l +++ g +++++ a ++r+e ++a+ +++l+ ++ ++++a+L+R+n+q+r +ee L++ +iP ++vg++ f++r ei+d+la+ +l +np d+++l+ri+ +p rgigd+ l+++ + a +++ ++l+++ ++++ ++ + k+ +f l+e + + +++ +++++++ ++e +g+ +ll+++ +eg+ +lenl+el+++++e++++++n s+ dfl + +l s ++ ++ + +daV++mT+H+aKGLEfpvVF++g+e+g +Ps+ i e +eeErRlfYV+iTRA+++L +taa+
#PP 589******************.....******************.******************************************************************************************************************************7...56666666777777799999999998.557789***********************************************************99987766655534356667779**********************************99**************************987
#SEQ YMLEHNYRSSARVLEAANKLI-----ENNTERLDKTLKPVKEAG-QPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACA---NAAEQNILDRGAHKATEFAGLMEAMS-EAADNYEPAAFLRFVMETSGYLDLLRQEgQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRtkaENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIaEGPSGIEEERRLFYVGITRAMERLLMTAAQ
#CS EEE-EESSS-HHHHHHHHHHHCC---TTSSSSCCCEEEESSTEEESSEEEEEECSHHHHHHHHHHHHHHHHHTTS-GGGEEEEESSCHHHHHHHHHHHHTTS-EEESSSSCGGGSHHHHHHHHHHHHHH-TTSHHHHHHHTTSTTCTTTHHHHHHHHHHHHHTTS-HHHHHH..HCHHTSCSTCHHHHHHHHHHHHHHHHHHHHCTTS-HHHHHHHHHHHTTHHHHHHCS.HHHHHHHHHHHHHHHHHHHHCCCSCSSCHHHHHHHHHHHHTCCCTSTT...SXXTTCCGSEEEEECGGGTT--EEEEEEETTBTBTTTBHHHH.HHHHHHHHHHHHHHHHHHTEEEEEEEEEEC